Dataset Information

An integration framework for linking avifauna niche and forest landscape models.

ABSTRACT: Avian cavity nesters (ACN) are viable indicators of forest structure, composition, and diversity. Utilizing these species responses in multi-disciplinary climate-avian-forest modeling can improve climate adaptive management. We propose a framework for integrating and evaluating climate-avian-forest models by linking two ACN niche models with a forest landscape model (FLM), LANDIS-II. The framework facilitates the selection of available ACN models for integration, evaluation of model transferability, and evaluation of successful integration of ACN models with a FLM. We found selecting a model for integration depended on its transferability to the study area (Northern Rockies Ecoregion of Idaho in the United States), which limited the species and model types available for transfer. However, transfer evaluation of the tested ACN models indicated a good fit for the study area. Several niche model variables (canopy cover, snag density, and forest cover type) were not directly informed by the LANDIS-II model, which required secondary modeling (Random Forest) to derive values from the FLM outputs. In instances where the Random Forest models performed with a moderate classification accuracy, the overall effect on niche predictions was negligible. Predictions based on LANDIS-II simulations performed similarly to predictions based on the niche model's original training input types. This supported the conclusion that the proposed framework is viable for informing avian niche models with FLM simulations. Even models that poorly approximate habitat suitability, due to the inherent constraints of predicting spatial niche use of irruptive species produced informative results by identifying areas of management focus. This is primarily because LANDIS-II estimates spatially explicit variables that were unavailable over large spatial extents from alternative datasets. Thus, without integration, one of the ACN niche models was not applicable to the study area. The framework will be useful for integrating avifauna niche and forest ecosystem models, which can inform management of contemporary and future landscapes under differing management and climate scenarios.

SUBMITTER: Walsh ES

PROVIDER: S-EPMC6555514 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

An integration framework for linking avifauna niche and forest landscape models.

Walsh Eric S ES Hudiburg Tara T

PloS one 20190607 6

Avian cavity nesters (ACN) are viable indicators of forest structure, composition, and diversity. Utilizing these species responses in multi-disciplinary climate-avian-forest modeling can improve climate adaptive management. We propose a framework for integrating and evaluating climate-avian-forest models by linking two ACN niche models with a forest landscape model (FLM), LANDIS-II. The framework facilitates the selection of available ACN models for integration, evaluation of model transferabil ...[more]

PMID: 31173586

Similar Datasets

Project description:Forested lands in the western USA have undergone changes in management and condition that are resulting in a shift towards climax vegetation. These changes can influence the quality and quantity of forage for herbivores that rely on early-seral plants. To evaluate how management of forested landscapes might affect nutrition for Shiras moose (A. a. shirasi) at large spatial scales, we focused on shrubs and evaluated summer diet composition, forage availability, and forage quality across 21 population management units encompassing >36,000 km2 in northern Idaho, USA. We identified 17 shrub species in the diets of moose, 11 of which comprised the bulk of the diets. These forage shrubs varied markedly in both energy (mean digestible energy for leaves ranged from 9.62 to 12.89 kJ/g) and protein (mean digestible protein for leaves ranged from 1.73 to 7.90%). By adapting established field sampling methods and integrating recent advances in remote sensing analyses in a modeling framework, we predicted approximations of current and past (i.e., 1984) quantities of forage shrubs across northern Idaho. We also created a qualitative index of population trend for moose across population management units using harvest data. Predicted quantities of forage shrubs varied widely across the study area with generally higher values at more northern latitudes. The quantity of forage shrubs was estimated to have declined over the past 30 years in about half of the population management units, with the greatest declines predicted for high-energy forage species. The population trend index was correlated with the percent change in availability of moderate-energy forage shrubs, indicating that availability of forage shrubs and change in availability over time might be affecting population dynamics for moose in northern Idaho. Our study highlights the importance of assessing how changes in forest management across broad spatiotemporal extents could affect wildlife and their habitats.

Project description:BACKGROUND:Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representing biomolecules as nodes and their interactions as edges. Very often the input data come from various sorts of omics analyses. Those resulting networks sometimes describe a wide range of aspects, for example different experiment conditions, species, tissue types, stimulating factors, mutants, or simply distinct interaction features of the same network produced by different algorithms. For these scenarios, synchronous visualization of more than one distinct network is an excellent mean to explore all the relevant networks efficiently. In addition, complementary analysis methods are needed and they should work in a workflow manner in order to gain maximal biological insights. RESULTS:In order to address the aforementioned needs, we have developed a Synchronous Network Data Integration (SyNDI) framework. This framework contains SyncVis, a Cytoscape application for user-friendly synchronous and simultaneous visualization of multiple biological networks, and it is seamlessly integrated with other bioinformatics tools via the Galaxy platform. We demonstrated the functionality and usability of the framework with three biological examples - we analyzed the distinct connectivity of plasma metabolites in networks associated with high or low latent cardiovascular disease risk; deeper insights were obtained from a few similar inflammatory response pathways in Staphylococcus aureus infection common to human and mouse; and regulatory motifs which have not been reported associated with transcriptional adaptations of Mycobacterium tuberculosis were identified. CONCLUSIONS:Our SyNDI framework couples synchronous network visualization seamlessly with additional bioinformatics tools. The user can easily tailor the framework for his/her needs by adding new tools and datasets to the Galaxy platform.

Project description:BackgroundExplanations for patterns observed in the structure of local assemblages are frequently sought with reference to interactions between species, and between species and their local environment. However, analyses of null models, where non-interactive local communities are assembled from regional species pools, have demonstrated that much of the structure of local assemblages remains in simulated assemblages where local interactions have been excluded. Here we compare the ability of two null models to reproduce the breeding bird community of Eastern Wood, a 16-hectare woodland in England, UK. A random draw model, in which there is complete annual replacement of the community by immigrants from the regional pool, is compared to a locally neutral community model, in which there are two additional parameters describing the proportion of the community replaced annually (per capita death rate) and the proportion of individuals recruited locally rather than as immigrants from the regional pool.ResultsBoth the random draw and locally neutral model are capable of reproducing with significant accuracy several features of the observed structure of the annual Eastern Wood breeding bird community, including species relative abundances, species richness and species composition. The two additional parameters present in the neutral model result in a qualitatively more realistic representation of the Eastern Wood breeding bird community, particularly of its dynamics through time. The fact that these parameters can be varied, allows for a close quantitative fit between model and observed communities to be achieved, particularly with respect to annual species richness and species accumulation through time.ConclusionThe presence of additional free parameters does not detract from the qualitative improvement in the model and the neutral model remains a model of local community structure that is null with respect to species differences at the local scale. The ability of this locally neutral model to describe a larger number of woodland bird communities with either little variation in its parameters or with variation explained by features local to the woods themselves (such as the area and isolation of a wood) will be a key subsequent test of its relevance.

Dataset Information

An integration framework for linking avifauna niche and forest landscape models.

Publications

An integration framework for linking avifauna niche and forest landscape models.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure